# run_fceri_gamma2.bngl # load and run FCERI model (gamma2 variant) using NF, HPP and SSA methods version("2.2.4+") setModelName("fceri_gamma2") readFile({file=>"fceri_gamma2.bngl",allow_actions=>0}) # configure HPP begin parameters # fraction of cell to simulate f 0.001 # population lumping rate, /s k_lump 10000 end parameters begin population maps # HPP1 only lumps free ligand Lig(l,l) -> X0001() k_lump # HPP6 also lumps the following Lyn(U,SH2) -> X0002() k_lump Syk(tSH2,l~Y,a~Y) -> X0003() k_lump Syk(tSH2,l~Y,a~pY) -> X0004() k_lump Syk(tSH2,l~pY,a~Y) -> X0005() k_lump Syk(tSH2,l~pY,a~pY) -> X0006() k_lump end population maps # actions: saveConcentrations() # simulate with NFsim #prefix=>"fceri_gamma2", simulate_nf({ suffix=>"nf", t_end=>1200, n_steps=>120, gml=>10000000, complex=>1, get_final_state=>0 }) # generate partial network and simulate with HPP resetConcentrations() generate_hybrid_model({ suffix=>"hpp", overwrite=>1, verbose=>1, execute=>1,\ actions=>["simulate_nf({ t_end=>1200, n_steps=>120 ,gml=>10000000, complex=>0 })"] }) # generate reaction network and simulate with SSA resetConcentrations() generate_network({ overwrite=>1, max_iter=>2 }) simulate_ssa({ suffix=>"ssa", t_end=>1200,n_steps=>120, print_CDAT=>0 })